FOWLER, Calif. — The oranges floating through the chlorine solution in the Bee Sweet Citrus Inc. packing plant will soon be packed in boxes stamped with name brands such as Dole and then shipped off to supermarkets across the country or to destinations in Japan, South Korea and other foreign points.

The chlorine bath, one of the first steps the oranges go through after arriving at the plant, is supposed to rid them of any harmful bacteria. In fact, fresh oranges have a sterling food safety record, but that’s not enough to exempt them and other fruit with little history of outbreaks from food safety regulations.

The Food and Drug Administration has proposed new agricultural standards that will require growers of dozens of varieties of fresh fruits and vegetables, including citrus, to take costly steps to prevent raw produce from being contaminated with harmful bacteria.

The FDA’s decision on which types of produce should be subject to the standards — and which are exempt — has emerged as one of the most controversial rules the agency faces as it implements the wide-ranging requirements of the Food Safety Modernization Act (PL 111-353).

Congress passed the law in response to a series of outbreaks involving raw produce, mainly greens that are grown close to the ground and easily contaminated by irrigation water or manure fertilizer. Growers of a variety of fruit say the new requirements for water testing, documentation, wildlife control and other measures will be costly and unnecessary, especially for crops such as oranges that are grown above the ground, cleansed during packing and peeled before being eaten.

Will Duane Scarlett, who grows apples, pears and cherries in Washington state, wrote to the FDA recently that the produce standards could put him out of business, even though the irrigation water he uses doesn’t come into contact with the fruit.

“With our nation’s desire to consume produce grown locally, I think there needs to be an exemption for these crops that are not grown on the soil surface,” he said.

The water-testing requirements alone could cost California orange and lemon producers more than $80 million a year, said Joel Nelsen, president of California Citrus Mutual, a trade group that represents the industry. Trying to control wildlife, which can contaminate crops by defecating on them, is impractical. In California, groves typically aren’t fenced in, partly because of the need to get equipment in and out easily.

“You have a regulation that was passed, and then after the fact we’re putting the details in on it, and the details happen to be quite onerous,” said Kevin Severns, who manages the Orange Cove-Sanger Citrus Association, a member group of Sunkist Growers in California’s San Joaquin Valley.

But in the FDA’s view, just because a fruit or vegetable hasn’t had an outbreak traced to it doesn’t mean it can’t. Agency officials say they based their list of commodities that would be covered by the proposed produce standards on research as to which foods are commonly eaten raw. Consumer advocates don’t think the list is long enough. Kale, which can be chopped to make a raw salad, and figs are exempt, for example.

The FDA claimed kale “is only eaten cooked. What restaurants do they eat at? Not the same ones I do,” said Jean Halloran, director of food policy initiatives for Consumers Union, publisher of Consumer Reports. “I am still working on what the criteria should be” for regulating commodities, “but Google returned me several million items for raw-kale recipes.”

The FDA was right to include fresh citrus, in part because lemons are so often cut into slices for beverages, she said in an email.

Some other consumer advocates are urging the FDA not to write the list of commodities into the rule itself, because the lengthy process of rule-making will make it harder to add items to the regulations later. “Instead, any list they develop should be included in accompanying documentation or guidance documents,” said Chris Waldrop, director of the Food Policy Institute at the Consumer Federation of America.

The citrus industry’s concern isn’t necessarily that the fruits were included in the regulations but that the industry fears it will be subject to requirements it believes are unnecessary.

“From a practical standpoint, do you want to be excluded and have everybody point fingers at you?” Nelsen asks rhetorically. “Should we be required to document what we do from a food safety perspective? Yeah, we’ll do that. It’s a positive story.”

The produce industry thought the proposed rule’s requirements would distinguish between higher- and lower-risk commodities. Instead, the agency’s proposed approach essentially treats all produce the same, putting the onus on growers to present data proving that their crops don’t pose a significant risk and merit being exempt from the new requirements, said Edward Ruckert, a lawyer with McDermott Will and Emery who advises the food industry.

Fruit and vegetable producers will have to explain to the FDA “why the regulations shouldn’t apply” to them, Ruckert said. “The first answer, that we haven’t had an issue, I’m not sure that FDA is going to be that receptive to. . . . They knew that going in. You’re not giving them any new information.”

The citrus industry has commissioned research that could show there is minimal contamination on the fruit because of the way it’s grown and the various prevention measures that packers such as Bee Sweet undertake. In addition to the chlorine bath, the fruit is also scrubbed and pressure-washed, and then inspected to ensure there aren’t breaks in the skin.

“There has not been a lot of research done on [citrus] because they don’t have an outbreak to contend with that has gotten the industry’s attention,” said Trevor Suslow, a University of California at Davis plant pathologist working on the project. As part of the research, oranges will be deliberately contaminated with bacteria so that scientists can determine whether they would still be present after the fruit goes through the packing process.

Other fruits that are grown above the ground, including table grapes, also have a good safety record, he said. Having a smooth surface on the fruit also makes a difference, even for a crop grown near the ground. For instance, honeydew melons have a good record, unlike cantaloupes, where the rough surface can and does harbor bacteria, Suslow said.